UMAP projections show sample groups (left), cell type annotations (middle), and CHIKV+ cells (right).



The fraction of cells passing QC filtering cutoffs is shown for each sample.




Macrophages


Subset annotations

UMAP projections show macrophage subsets.



Module scores for Culemann et al. gene lists are shown for each macrophage cluster. Clusters are colored based on the assigned subset labels.



Heatmaps show mean expression of Culemann et al. gene lists. Replicates are shown separately for each macrophage subset.

CCR2_ARG1_infiltrating




CCR2_IL1B_infiltrating




CX3CR1_lining




RELMa_interstitial




AQP1_interstitial




CHIKV+ cells

UMAP projections show CHIKV+ cells (left) and CHIKV-high clusters (middle, right) for CHIKV-infected samples.



The fraction of cells that are CHIKV+ is shown for each replicate from each macrophage subset. P values were calculated by pooling replicates together, using a hypergeometric test with Bonferroni correction.



The fraction of CHIKV+ cells passing QC filtering cutoffs is shown for each sample.




Differential expression

Top 50 upregulated genes associated with inflammatory disease are shown below for mock- vs CHIKV-infected macrophages.



Genes associated with antigen presentation via MHC class II are shown below. Boxplots compare expression in mock (light) vs CHIKV (dark) for each macrophage subset.



Top genes upregulated in CHIKV-infected mice are shown below for each macrophage subset.

Upset plots (top) show the overlap between differentially expressed genes identified for each subset. Subsets with overlapping genes are connected by a black line, bars show the number of genes. A single point (not connected by a black line) shows the number of unique genes for the subset.

AQP1_interstitial




CX3CR1_lining




infiltrating




RELMa_interstitial




unassigned




Simmons et al. 

Expression of Simmons et al. gene lists is shown below.

SLAMF7_stim




SLAMF7_high




arthritis




T cells


Subset annotations

UMAP projections show T cell subsets.



Key markers are shown below for T cells from mock- and CHIKV-infected samples.




Differential expression

Genes upregulated in CHIKV vs mock-infected mice are shown below, all T cells were grouped together.



Genes upregulated in T cells from CHIKV vs mock-infected mice are shown below. All CD4+ or CD8+ T cells were grouped together.



Ifng expression is shown below for each T cell subset.